infer_grn errors

[bjstewart1]

infer_grn() is giving me this error Error in tf_g_cor[unique(tfs_use), , drop = F] : object of type 'S4' is not subsettable

is this the problem? tf_g_cor <- as(sparse_cor(tf_x, g_x), 'generalMatrix')

R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: /nfs/team297/bs16/tools/conda_envs/r_pando/lib/libopenblasp-r0.3.24.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/London
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] MatrixGenerics_1.14.0             matrixStats_1.1.0                
 [3] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.1                  
 [5] BiocIO_1.12.0                     Biostrings_2.70.1                
 [7] XVector_0.42.0                    dplyr_1.1.3                      
 [9] rtracklayer_1.62.0                EnsDb.Hsapiens.v86_2.99.0        
[11] ensembldb_2.26.0                  AnnotationFilter_1.26.0          
[13] GenomicFeatures_1.54.1            AnnotationDbi_1.64.1             
[15] Biobase_2.62.0                    GenomicRanges_1.54.1             
[17] GenomeInfoDb_1.38.1               IRanges_2.36.0                   
[19] S4Vectors_0.40.1                  BiocGenerics_0.48.1              
[21] SeuratObject_4.1.4                Seurat_4.3.0                     
[23] Signac_1.11.0                     Pando_1.0.5                      
[25] reticulate_1.34.0                

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.34.0         spatstat.sparse_3.0-3      
  [3] bitops_1.0-7                DirichletMultinomial_1.44.0
  [5] TFBSTools_1.40.0            httr_1.4.7                 
  [7] RColorBrewer_1.1-3          tools_4.3.2                
  [9] sctransform_0.4.1           utf8_1.2.4                 
 [11] R6_2.5.1                    lazyeval_0.2.2             
 [13] uwot_0.1.16                 withr_2.5.2                
 [15] sp_2.1-1                    prettyunits_1.2.0          
 [17] gridExtra_2.3               progressr_0.14.0           
 [19] cli_3.6.1                   spatstat.explore_3.2-5     
 [21] spatstat.data_3.0-3         readr_2.1.4                
 [23] ggridges_0.5.4              pbapply_1.7-2              
 [25] Rsamtools_2.18.0            R.utils_2.12.2             
 [27] dichromat_2.0-0.1           parallelly_1.36.0          
 [29] maps_3.4.1.1                RSQLite_2.3.3              
 [31] pals_1.8                    generics_0.1.3             
 [33] gtools_3.9.4                ica_1.0-3                  
 [35] spatstat.random_3.2-1       GO.db_3.18.0               
 [37] Matrix_1.6-3                fansi_1.0.5                
 [39] abind_1.4-5                 R.methodsS3_1.8.2          
 [41] lifecycle_1.0.4             yaml_2.3.7                 
 [43] SummarizedExperiment_1.32.0 SparseArray_1.2.2          
 [45] BiocFileCache_2.10.1        Rtsne_0.16                 
 [47] grid_4.3.2                  blob_1.2.4                 
 [49] promises_1.2.1              crayon_1.5.2               
 [51] miniUI_0.1.1.1              lattice_0.22-5             
 [53] cowplot_1.1.1               annotate_1.80.0            
 [55] KEGGREST_1.42.0             mapproj_1.2.11             
 [57] pillar_1.9.0                rjson_0.2.21               
 [59] future.apply_1.11.0         codetools_0.2-19           
 [61] fastmatch_1.1-4             leiden_0.4.3               
 [63] glue_1.6.2                  data.table_1.14.8          
 [65] vctrs_0.6.4                 png_0.1-8                  
 [67] spam_2.10-0                 gtable_0.3.4               
 [69] poweRlaw_0.70.6             cachem_1.0.8               
 [71] S4Arrays_1.2.0              mime_0.12                  
 [73] tidygraph_1.2.3             pracma_2.4.4               
 [75] survival_3.5-7              RcppRoll_0.3.0             
 [77] ellipsis_0.3.2              fitdistrplus_1.1-11        
 [79] ROCR_1.0-11                 nlme_3.1-163               
 [81] bit64_4.0.5                 progress_1.2.2             
 [83] filelock_1.0.2              RcppAnnoy_0.0.21           
 [85] irlba_2.3.5.1               KernSmooth_2.23-22         
 [87] colorspace_2.1-0            seqLogo_1.68.0             
 [89] DBI_1.1.3                   tidyselect_1.2.0           
 [91] bit_4.0.5                   compiler_4.3.2             
 [93] curl_5.1.0                  xml2_1.3.5                 
 [95] DelayedArray_0.28.0         plotly_4.10.3              
 [97] scales_1.2.1                caTools_1.18.2             
 [99] lmtest_0.9-40               rappdirs_0.3.3             
[101] stringr_1.5.1               digest_0.6.33              
[103] goftest_1.2-3               spatstat.utils_3.0-4       
[105] motifmatchr_1.24.0          htmltools_0.5.7            
[107] pkgconfig_2.0.3             sparseMatrixStats_1.14.0   
[109] dbplyr_2.4.0                fastmap_1.1.1              
[111] rlang_1.1.2                 htmlwidgets_1.6.2          
[113] shiny_1.7.5.1               farver_2.1.1               
[115] zoo_1.8-12                  jsonlite_1.8.7             
[117] BiocParallel_1.36.0         R.oo_1.25.0                
[119] RCurl_1.98-1.13             magrittr_2.0.3             
[121] GenomeInfoDbData_1.2.11     dotCall64_1.1-0            
[123] patchwork_1.1.3             munsell_0.5.0              
[125] Rcpp_1.0.11                 viridis_0.6.4              
[127] stringi_1.8.1               ggraph_2.1.0               
[129] zlibbioc_1.48.0             MASS_7.3-60                
[131] plyr_1.8.9                  parallel_4.3.2             
[133] listenv_0.9.0               ggrepel_0.9.4              
[135] deldir_1.0-9                CNEr_1.38.0                
[137] graphlayouts_1.0.2          splines_4.3.2              
[139] tensor_1.5                  hms_1.1.3                  
[141] igraph_1.5.1                spatstat.geom_3.2-7        
[143] reshape2_1.4.4              biomaRt_2.58.0             
[145] TFMPvalue_0.0.9             XML_3.99-0.15              
[147] tzdb_0.4.0                  tweenr_2.0.2               
[149] httpuv_1.6.12               grr_0.9.5                  
[151] RANN_2.6.1                  tidyr_1.3.0                
[153] purrr_1.0.2                 polyclip_1.10-6            
[155] future_1.33.0               scattermore_1.2            
[157] ggplot2_3.4.4               ggforce_0.4.1              
[159] xtable_1.8-4                restfulr_0.0.15            
[161] later_1.3.1                 viridisLite_0.4.2          
[163] ggpointdensity_0.1.0        tibble_3.2.1               
[165] memoise_2.0.1               GenomicAlignments_1.38.0   
[167] cluster_2.1.4               globals_0.16.2